/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef itkKappaSigmaThresholdImageCalculator_hxx
#define itkKappaSigmaThresholdImageCalculator_hxx
#include "itkKappaSigmaThresholdImageCalculator.h"

#include "itkImageRegionConstIteratorWithIndex.h"
#include "itkImageRegionConstIterator.h"

namespace itk
{
template <typename TInputImage, typename TMaskImage>
KappaSigmaThresholdImageCalculator<TInputImage, TMaskImage>::KappaSigmaThresholdImageCalculator()
  : m_MaskValue(NumericTraits<MaskPixelType>::max())
  , m_Output(NumericTraits<InputPixelType>::ZeroValue())
{}

template <typename TInputImage, typename TMaskImage>
void
KappaSigmaThresholdImageCalculator<TInputImage, TMaskImage>::Compute()
{
  if (!this->m_Image)
  {
    return;
  }

  // Initialize the values
  InputPixelType threshold = NumericTraits<InputPixelType>::max(); // use all
                                                                   // the
                                                                   // pixels
                                                                   // to begin

  for (unsigned int iteration = 0; iteration < this->m_NumberOfIterations; iteration++)
  {
    ImageRegionConstIteratorWithIndex<InputImageType> iIt(this->m_Image, this->m_Image->GetRequestedRegion());

    // Compute the mean
    iIt.GoToBegin();
    SizeValueType count = 0;
    double        mean = 0;
    while (!iIt.IsAtEnd())
    {
      if (!this->m_Mask || this->m_Mask->GetPixel(iIt.GetIndex()) == this->m_MaskValue)
      {
        const InputPixelType & v = iIt.Get();
        if (v <= threshold)
        {
          mean += v;
          count++;
        }
      }
      ++iIt;
    }
    mean = mean / count;

    // Compute sigma
    iIt.GoToBegin();
    double sigma = 0;
    while (!iIt.IsAtEnd())
    {
      if (!this->m_Mask || this->m_Mask->GetPixel(iIt.GetIndex()) == this->m_MaskValue)
      {
        const InputPixelType & v = iIt.Get();
        if (v <= threshold)
        {
          sigma += itk::Math::sqr(v - mean);
        }
      }
      ++iIt;
    }
    sigma = std::sqrt(sigma / (count - 1));

    // Compute the threshold for the next iteration
    auto newThreshold = static_cast<InputPixelType>(mean + this->m_SigmaFactor * sigma);
    if (newThreshold == threshold)
    {
      // No need to continue - the threshold is the same and will produce the
      // same result
      break;
    }
    threshold = newThreshold;
  }

  this->m_Output = threshold;
  this->m_Valid = true;
}

template <typename TInputImage, typename TMaskImage>
const typename KappaSigmaThresholdImageCalculator<TInputImage, TMaskImage>::InputPixelType &
KappaSigmaThresholdImageCalculator<TInputImage, TMaskImage>::GetOutput() const
{
  if (!this->m_Valid)
  {
    itkExceptionMacro(<< "GetOutput() invoked, but the output have not been computed. Call Compute() first.");
  }
  return this->m_Output;
}

template <typename TInputImage, typename TMaskImage>
void
KappaSigmaThresholdImageCalculator<TInputImage, TMaskImage>::PrintSelf(std::ostream & os, Indent indent) const
{
  Superclass::PrintSelf(os, indent);

  os << indent << "Valid: " << this->m_Valid << std::endl;
  os << indent << "MaskValue: " << this->m_MaskValue << std::endl;
  os << indent << "SigmaFactor: " << this->m_SigmaFactor << std::endl;
  os << indent << "NumberOfIterations: " << this->m_NumberOfIterations << std::endl;

  os << indent << "Output: " << static_cast<typename itk::NumericTraits<InputPixelType>::PrintType>(m_Output)
     << std::endl;

  itkPrintSelfObjectMacro(Image);
  itkPrintSelfObjectMacro(Mask);
}
} // end namespace itk

#endif
